Digital Commons Network^™

Information Infrastructure For Integrated Ecohydraulic And Water Resources Modeling And Assessment, R. Wallace, K. Pathak, M. Fife, Norman L. Jones, J. P. Holland, D. Stuart, J. Harris, C. Butler, D. R. Richards

Faculty Publications

Watershed management increasingly requires ecohydraulic modeling and assessment within a regional context, rather than on a project-by-project basis. Such holistic modeling and assessment require evaluation capabilities across multiple temporal and spatial scales. Thus, modeling and assessment tools must be integrated in a scientifically and computationally effective infrastructure. The US Army Engineer Research and Development Center, in concert with the Hydrologic Engineering Center and its academic partners, including Brigham Young University, is establishing a comprehensive set of hydroinformatics modeling and assessment tools for ecohydraulic and water resources management applications, all linked based on a common data and information infrastructure. This paper …

A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron J. Adams, U. Gozel, K. B. Nguyen, R. N. Inserra, R. M. Giblin-Davis

Faculty Publications

The D2-D3 and ITS regions of rDNA from 33 Florida populations of Belonolaimus spp. were sequenced and subjected to phylogenetic analysis. Our objective was to derive a theoretical evolutionary framework for interpreting phenotypic differences as they relate to the taxonomy of the genus. The most striking aspect of the phylogenetic analysis is that none of the three nominal species (B. longicaudatus, B. euthychilus, and B. gracilis) are monophyletic. Additionally, two taxa appear to have discordant ITS and LSU sequences. Three major clades of B. longicaudatus exhibited discernible, overlapping, geographic foci from east to west across the peninsula. Morphological character states …

The Smith-Mundt Act's Ban On Domestic Propaganda: An Analysis Of The Cold War Statute Limiting Access To Public Diplomacy, Edward L. Carter, Allen W. Palmer

Faculty Publications

For more than fifty years, the U.S. Code has authorized the federal government to disseminate messages about America to international audiences. For at least thirty years, federal law has also prohibited those international propaganda messages from being disseminated within the United States. Given the realities of the acceleration and dispersion of information flow across international borders in the twenty-first century, a ban on dissemination of information that is tied to geographic boundaries raises both practical and policy issues. The domestic dissemination ban may have outlived its usefulness and relevance. Further, futile enforcement of the statute contradicts general U.S. policy promoting …

A Review Of Polylekithum Arnold, 1934 And Its Familial Affinities Using Morphological And Molecular Data, With Description Of Polylekithum Catahoulensis Sp Nov., Stephen S. Curran, Vasyl V. Tkach, Robin M. Overstreet

Faculty Publications

The type material of Polylekithum ictaluri, P. halli, and Maculifer chandleri was examined from the United States National Parasite Museum, and we determined that the material was conspecific, making P. halli and M. chandleri junior subjective synonyms of P. ictaluri. Polylekithum catahoulensis sp. nov. was described from material collected from catfishes at the Catahoula Wildlife Refuge, LaSalle Parish, Louisiana, USA, and compared with P. ictaluri collected from catfishes in Reelfoot Lake, Obion County, Tennessee, USA, and the Pearl River, Hancock County, Mississippi, USA. Polylekithum catahoulensis had smaller eggs (77–88 μm long by 51–63 μm wide vs. 94–108 μm by …

Indeterminacy And Society By Russell Hardin, Daniel R. Sabia

Faculty Publications

No abstract provided.

A Novel Account Of Scientific Anomaly: Help For The Dispute Over Low-Dose Biochemical Effects, Kevin C. Elliott

Faculty Publications

The biological effects of low doses of toxic and carcinogenic chemicals are currently a matter of significant scientific controversy. This paper argues that philosophers of science can contribute to alleviating this controversy by examining it with the aid of a novel account of scientific anomaly. Specifically, analysis of contemporary research on chemical hormesis (i.e.. alleged beneficial biological effects produced by low doses of substances that are harmful at higher doses) suggests that scientists may initially describe anomalous phenomena in terms of multiple distinct '"characterizations," each
of which is compatible with current empirical evidence. By focusing attention on this feature of …

Theory Of Cavity-Polariton Self-Trapping And Optical Strain In Polymer Chains, M. V. Katkov, Yuriy V. Pershin Dr, C. Piermarocchi

Faculty Publications

We consider a semiconductor polymer chain coupled to a single electromagnetic mode in a cavity. The excitations of the chain have a mixed exciton-photon character and are described as polaritons. Polaritons are coupled to the lattice by the deformation potential interaction and can propagate in the chain. We find that the presence of optical excitation in the polymer induces strain on the lattice. We use a BCS variational wave function to calculate the chemical potential of the polaritons as a function of their density. We analyze first the case of a short chain with only two unit cells in order …

Vision-Based Target Geo-Location Using A Fixed-Wing Miniature Air Vehicle, D. Blake Barber, Joshua D. Redding, Timothy W. Mclain, Randal W. Beard, Clark N. Taylor

Faculty Publications

This paper presents a method for determining the GPS location of a ground-based object when imaged from a fixed-wing miniature air vehicle (MAV). Using the pixel location of the target in an image, with measurements of MAV position and attitude, and camera pose angles, the target is localized in world coordinates. The main contribution of this paper is to present four techniques for reducing the localization error. In particular, we discuss RLS filtering, bias estimation, flight path selection, and wind estimation. The localization method has been implemented and flight tested on BYU’s MAV testbed and experimental results are presented demonstrating …

Objectively Measured Physical Activity In Sixth-Grade Girls, Russell R. Pate, June Stevens, Charlotte Pratt, James F. Sallis, Kathryn H. Schmitz, Larry S. Webber, Gregory J. Welk, Deborah Rohm Young

Faculty Publications

Objectives - To describe the objectively-measured physical activity (PA) characteristics of a diverse sample of 6^th grade girls to examine influences on PA, and to report compliance with PA guidelines.

Design - Cross-sectional study.

Setting - Six locations across the United States.

Participants - 1578 6^th grade girls. Actigraph accelerometers were worn for 7 days, and data for 6 days were included in the analyses.

Main exposure - Race/ethnicity, free-or-reduced price lunch (FRPL), and geographic region.

Main outcome measure - Six operational definitions of adequate activity (60 min or 30 min of daily MVPA at or above 4.6, …

The Central Laser Facility At The Pierre Auger Observatory, B. Fick, M. Malek, J. A.J. Matthews, J. Matthews, R. Meyhandan, M. Mostafá, M. Roberts, P. Sommers, L. Wiencke

Faculty Publications

The Central Laser Facility is located near the middle of the Pierre Auger Observatory in Argentina. It features an ultraviolet laser and optical components that direct a beam of calibrated, pulsed light into the sky. Light scattered from this beam produces tracks in the Auger optical detectors, which normally record nitrogen fluorescence tracks from cosmic ray air showers. The Central Laser Facility acts as a "test beam" that is used to investigate properties of the atmosphere and the air fluorescence detectors. Additionally, the laser can send a light pulse via optical fiber to the nearest surface detector tank. This signal, …

Linking Bacterioplankton Community Structures To Environmental State Variables And Phytoplankton Assemblages In Two South Carolina Salt Marsh Estuaries, Wes Johnson, Alan J. Lewitus, Madilyn Fletcher

Faculty Publications

Microorganisms are among the most important organisms to the ecology of salt marsh estuaries; however, fundamental questions regarding their distribution, environmental controls, and interactions with phytoplankton remain unanswered. We used denaturing gradient gel electrophoresis (DGGE) of bacterial rRNA genes and high performance liquid chromatography (HPLC) of phytoplankton photopigments to characterize planktonic communities from the Ashepoo, Combahee, and Edisto (ACE) Basin and North Inlet (NI) estuaries on the South Carolina coast, USA. Multivariate comparisons of the planktonic community profiles revealed that the 2 estuaries supported distinct bacterial communities. Furthermore, bacterial communities in both systems were partitioned into separate particle-associated (PA) and …

Emergence Of Primate Genes By Retrotransposon-Mediated Sequence Transduction, Jinchuan Xing, Hui Wang, Victoria P. Belancio, Richard Cordaux, Prescott L. Deininger, Mark A. Batzer

Faculty Publications

Gene duplication is one of the most important mechanisms for creating new genes and generating genomic novelty. Retrotransposon-mediated sequence transduction (i.e., the process by which a retrotransposon carries flanking sequence during its mobilization) has been proposed as a gene duplication mechanism. L1 exon shuffling potential has been reported in cell culture assays, and two potential L1-mediated exon shuffling events have been identified in the genome. SVA is the youngest retrotransposon family in primates and is capable of 3′ flanking sequence transduction during retrotransposition. In this study, we examined all of the full-length SVA elements in the human genome to assess …

The Large‐Scale Freshwater Cycle Of The Arctic, Mark C. Serreze, Andrew P. Barrett, Andrew G. Slater, Rebecca A. Woodgate, Knut Aagaard, Richard B. Lammers, Michael Steele, Richard Moritz, Michael Meredith, Craig M. Lee

Faculty Publications

This paper synthesizes our understanding of the Arctic's large‐scale freshwater cycle. It combines terrestrial and oceanic observations with insights gained from the ERA‐40 reanalysis and land surface and ice‐ocean models. Annual mean freshwater input to the Arctic Ocean is dominated by river discharge (38%), inflow through Bering Strait (30%), and net precipitation (24%). Total freshwater export from the Arctic Ocean to the North Atlantic is dominated by transports through the Canadian Arctic Archipelago (35%) and via Fram Strait as liquid (26%) and sea ice (25%). All terms are computed relative to a reference salinity of 34.8. Compared to earlier estimates, …

Predicting On-Orbit Static Single Event Upset Rates In Xilinx Virtex Fpgas, Joshua Engel, Keith S. Morgan, Michael J. Wirthlin, Paul S. Graham

Faculty Publications

Sponsorship: Department of Energy, Los Alamos National Laboratory. This document describes the methodology used to predict single-event upset rates for Xilinx Virtex FPGAs based on the CREME96 orbit modeling tool. Using this methodology, SEU upset rates are obtained for several Xilinx Virtex FPGAs including Virtex, Virtex-II, and Virtex-4. Further, SEU upset rates are obtained for a variety of orbits for each of these FPGAs.

Simulation Of A Carbon Nanotube-Based Compliant Parallel-Guiding Mechanism: A Nanomechanical Building Block, Martin L. Culpepper, Christopher M. Dibiasio, Robert M. Panas, Spencer P. Magleby, Larry L. Howell

Faculty Publications

The authors report the behavior of a nanoscale parallel-guiding mechanism wherein the compliant components are single-walled carbon nanotubes. Parallel-guiding mechanisms are often the building blocks of macro- and microscale mechanical systems. The authors present results that provide insight into the performance of a parallel-guiding mechanism for nanoscale devices. The device exhibits a range over 75% of the device size, i.e., 5.5 nm, when actuated with 6.4 nN. Below 3.6 nN, displacements are due to bulk elastic bending of the nanotubes. Above 5.2 nN, displacements are governed by the hingelike bending of kinks in the nanotubes. van der Waals forces are …

Eliminating Redundant And Less-Informative Rss News Articles Based On Word Similarity And A Fuzzy Equivalence Relation, Ian Garcia, Yiu-Kai D. Ng

Faculty Publications

The Internet has marked this era as the information age. There is no precedent in the amazing amount of information, especially network news, that can be accessed by Internet users these days. As a result, the problem of seeking information in online news articles is not the lack of them but being overwhelmed by them. This brings huge challenges in processing online news feeds, e.g., how to determine which news article is important, how to determine the quality of each news article, and how to filter irrelevant and redundant information. In this paper, we propose a method for filtering redundant …

Tetrakis(N-Ethyl-9-Oxo-4-Azonia-5-Aza-9h-Fluorene) Tetra-Μ3-Iodo-Hexa-Μ2-Iodo-Dodecaiodohexabismuthate, Meredith A. Tershany, Andrea M. Goforth, Mark D. Smith, Leroy Peterson Jr., Hans-Conrad Zur Loye

Faculty Publications

The new iodobismuthate compound (C₁₃H₁₁N₂O)₄[Bi₆I₂₂] has been synthesized solvothermally by reacting BiI₃, Zn(NO₃)₂·6H₂O and 4,5-diazafluoren-9-one in a water/ethanol solvent mixture. The asymmetric unit of the compound contains two independent [N-ethyl-4,5-dafo]⁺ cations and one-half of a centrosymmetric [Bi₆I₂₂]^4- anion. The average terminal Bi-I, Bi-₂-I and Bi-₃-I bond lengths in the anion are 2.8923 (2), 3.1403 (2) and 3.3022 (2) Å, respectively.

Spatial Separation Of Large Dynamical Blueshift And Harmonic Generation, Mette B. Gaarde, Mitsuko Murakami, Reinhard Kienberger

Faculty Publications

We study the temporal and spatial dynamics of the large amplitude and frequency modulation that can be induced in an intense, few cycle laser pulse as it propagates through a rapidly ionizing gas. Our calculations include both single atom and macroscopic interactions between the nonlinear medium and the laser field. We analyze the harmonic generation by such pulses and show that it is spatially separated from the ionization dynamics which produce a large dynamical blueshift of the laser pulse. This means that small changes in the initial laser focusing conditions can lead to large differences in the laser frequency modulation, …

Electrophile-Induced Ether Transfer: A New Approach To Polyketide Structural Units, Kai Liu, Richard E. Taylor, Rendy Kartika

Faculty Publications

A strategically novel approach to the formation of syn-1,3-diol mono- and diethers through electrophilic activation of homoallylic alkoxymethyl ethers has been developed. The resulting polyketide-like synthetic fragments are generated in good yield and with excellent stereocontrol. A chairlike transition state is proposed to account for the high stereoselectivity. Varying the conditions of the reaction workup results in the efficient generation of mono- and diether containing structural units common to polyketide natural products. © 2006 American Chemical Society.

Subtidal Inner Shelf Currents Off Cartagena De Indias, Caribbean Coast Of Colombia, Mauro Maza, George Voulgaris, Bulusu Subrahmanyam

Faculty Publications

Seasonal trends in inner shelf subtidal circulation off the coast of Cartagena de Indias, Colombia, are examined through the analysis of current profiles, hydrographic, meteorological and satellite data collected from 1999 to 2002. During the dry season (December–April) the water column is well-mixed and along-shelf currents flow southwestward following the steady trade winds. In the rainy season (May –November) the water column experiences continuous events of stratification and the along-shelf currents flow northeastward, opposing the weak southwestward winds. In the dry season the along shelfcirculation is mostly driven by wind forcing, while in the rainy season, the circulation is set …

Nodal Structure Of Unconventional Superconductors Probed By Angle Resolved Thermal Transport Measurements, Y. Matsuda, K. Izawa, I. Vekhter

Faculty Publications

Over the past two decades, unconventional superconductivity with gap symmetry other than s wave has been found in several classes of materials, including heavy fermion, high Tc, and organic superconductors. Unconventional superconductivity is characterized by anisotropic superconducting gap functions, which may have zeros (nodes) along certain directions in the Brillouin zone. The nodal structure is closely related to the pairing interaction, and it is widely believed that the presence of nodes is a signature of magnetic or some other exotic, rather than conventional phonon mediated, pairing mechanism. Therefore experimental determination of the gap function is of fundamental importance. However, the …

Red Tides In The Gulf Of Mexico: Where, When, And Why?, J. J. Walsh, J. K. Jolliff, B. P. Darrow, J. M. Lenes, S.P. Milroy, A. Remsen, D.A. Dieterle, K.L. Carder, F.R. Chen, F.R. Chen, G.A. Vargo, R.H. Weisberg, K.A. Fanning, F.E. Muller-Karger, E. Shinn, K.A. Steidinger, C.A. Heil, C.R. Tomas, J.S. Prospero, T.N. Lee, G.J. Kirkpatrick, T.E. Whitledge, D.A. Stockwell, T.A. Villareal, A.E. Jochens, P.S. Bontempi

Faculty Publications

Independent data from the Gulf of Mexico are used to develop and test the hypothesis that the same sequence of physical and ecological events each year allows the toxic dinoflagellate Karenia brevis to become dominant. A phosphorus-rich nutrient supply initiates phytoplankton succession, once deposition events of Saharan iron-rich dust allow Trichodesmium blooms to utilize ubiquitous dissolved nitrogen gas within otherwise nitrogen-poor sea water. They and the co-occurring K. brevis are positioned within the bottom Ekman layers, as a consequence of their similar diel vertical migration patterns on the middle shelf. Upon onshore upwelling of these near-bottom seed populations to CDOM-rich …

Density Of States, Entropy, And The Superconducting Pomeranchuk Effect In Pauli-Limited Al Films, X. S. Wu, P. W. Adams, G. Catelani

Faculty Publications

We present low-temperature tunneling density of states measurements of Pauli-limited Al films in which the Zeeman and orbital contributions to the critical field are comparable. We show that films in the thickness range of 6-7 nm exhibit a reentrant parallel critical field transition which is associated with a high-entropy superconducting phase, similar to the high-entropy solid phase of He3 responsible for the Pomeranchuk effect. This phase is characterized by an excess of states near the Fermi energy so long as the parallel critical field transition remains second order. Theoretical fits to the zero-bias tunneling conductance are in good agreement with …

Further Evidence For Variable Synchrotron Emission In Xte J1118+480 In Outburst, R. I. Hynes, E. L. Robinson, K. J. Pearson, D. M. Gelino, W. Cui, Y. Q. Xue, M. A. Wood, T. K. Watson, D. E. Winget, I. M. Silver

Faculty Publications

We present simultaneous multicolor infrared and optical photometry of the black hole X-ray transient XTE Jill 8+480 during its short 2005 January outburst, supported by simultaneous X-ray observations. The variability is dominated by short timescales, ∼10 s, although a weak superhump also appears to be present in the optical. The optical rapid variations, at least, are well correlated with those in X-rays. Infrared JHKS photometry, as in the previous outburst, exhibits especially large-amplitude variability. The spectral energy distribution (SED) of the variable infrared component can be fitted with a power law of slope α = -0.78 ± 0.07, where Fν …

Large Deviations For The Two-Dimensional Navier-Stokes Equations With Multiplicative Noise, S. S. Sritharan, P. Sundar

Faculty Publications

A Wentzell-Freidlin type large deviation principle is established for the two-dimensional Navier-Stokes equations perturbed by a multiplicative noise in both bounded and unbounded domains. The large deviation principle is equivalent to the Laplace principle in our function space setting. Hence, the weak convergence approach is employed to obtain the Laplace principle for solutions of stochastic Navier-Stokes equations. The existence and uniqueness of a strong solution to (a) stochastic Navier-Stokes equations with a small multiplicative noise, and (b) Navier-Stokes equations with an additional Lipschitz continuous drift term are proved for unbounded domains which may be of independent interest. © 2006 Elsevier …

The Saccharomyces Cerevisiae Rna Polymerase Iii Recruitment Factor Subunits Brf1 And Bdp1 Impose A Strict Sequence Preference For The Downstream Half Of The Tata Box, Nick D. Tsihlis, Anne Grove

Faculty Publications

Association of the TATA-binding protein (TBP) with its cognate site within eukaryotic promoters is key to accurate and efficient transcriptional initiation. To achieve recruitment of Saccharomyces cerevisiae RNA polymerase III, TBP is associated with two additional factors, Brf1 and Bdp1, to form the initiation factor TFIIIB. Previous data have suggested that the structure or dynamics of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. We show here, using the altered specificity TBP mutant TBPm3 and an iterative in vitro selection assay, that entry of Brf1 and Bdp1 into the complex imposes a strict …

A Molecular Phylogenetic Analysis Of Strombid Gastropod Morphological Diversity, Jared M. Latiolais, Michael S. Taylor, Kaustuv Roy, Michael E. Hellberg

Faculty Publications

The shells of strombid gastropods show a wide variety of forms, ranging from small and fusiform to large and elaborately ornamented with a strongly flared outer lip. Here, we present the first species-level molecular phylogeny for strombids and use the resulting phylogenetic framework to explore relationships between species richness and morphological diversity. We use portions of one nuclear (325 bp of histone H3) and one mitochondrial (640 bp of cytochrome oxidase I, COI) gene to infer relationships within the two most species-rich genera in the Strombidae: Strombus and Lambis. We include 32 species of Strombus, representing 10 of 11 extant …

Geographic Variation In Clonal Structure In A Reef-Building Caribbean Coral, Acropora Palmata, Iliana B. Baums, Margaret W. Miller, Michael E. Hellberg

Faculty Publications

Species that build the physical structure of ecosystems often reproduce clonally, both in terrestrial (e.g., grasses, trees) and marine (e.g., corals, seagrasses) environments. The degree of clonality may vary over a species' range in accordance with the relative success of sexual and asexual recruitment. High genotypic (clonal) diversity of structural species may promote the species diversity and resilience of ecosystems in the face of environmental extremes. Conversely, low genotypic diversity may indicate an asexual strategy to maintain resources and genetic variation during population decline. Here, we use microsatellite markers to assess geographic variation in clonality in the coral Acropora palmata …

Siamese, A Plant-Specific Cell Cycle Regulator, Controls Endoreplication Onset In Arabidopsis Thaliana, Michelle L. Churchman, Matthew L. Brown, Naohiro Kato, Viktor Kirik, Martin Hülskamp, Dirk Inzé, Lieven De Veylder, Jason D. Walker, Ui Zheng, David G. Oppenheimer, Taylor Gwin, Jason Churchman, John C. Larkin

Faculty Publications

Recessive mutations in the SIAMESE (SIM) gene of Arabidopsis thaliana result in multicellular trichomes harboring individual nuclei with a low ploidy level, a phenotype strikingly different from that of wild-type trichomes, which are single cells with a nuclear DNA content of ∼16C to 32C. These observations suggested that SIM is required to suppress mitosis as part of the switch to endoreplication in trichomes. Here, we demonstrate that SIM encodes a nuclear-localized 14-kD protein containing a cyclin binding motif and a motif found in ICK/KRP (for interactors of Cdc2 kinase/Kip-related protein) cell cycle inhibitor proteins. Accordingly, SIM was found to associate …

An Organic White Light-Emitting Fluorophore, Youjun Yang, Mark Lowry, Corin M. Schowalter, Sayo O. Fakayode, Jorge O. Escobedo, Xiangyang Xu, Huating Zhang, Timothy J. Jensen, Frank R. Fronczek, Isiah M. Warner, Robert M. Strongin

Faculty Publications

The synthesis of new benzo[a]- and [b]xanthene dye frameworks is described. A unique benzo[a]xanthene, seminaphtho[a]fluorone (SNAFR-1), is studied in a variety of media. The optimization of solution parameters and excitation wavelengths allows SNAFR-1 to display red, green, and blue emission bands of approximately equal intensities and also to produce white light. Ratiometric red (anion) and green (neutral) emissions are observed upon varying solution pH. A pH-independent violet-blue emission band is due to the addition of nucleophiles to the benzylic carbon of SNAFR-1. © 2006 American Chemical Society.